source: branches/sina/HELP_SOURCE/source/arb.hlp

#       main topics:
UP      help.hlp
UP      copyright.hlp
UP      changes.hlp
UP      version.hlp
UP      arb.pdf
UP      glossary.hlp
UP      arb_commands.hlp
UP      FAQS.hlp
UP      copyNpaste.hlp

#       sub topics:
SUB     arb_ntree.hlp
SUB     e4.hlp
SUB     arb_pars.hlp
SUB     pt_server.hlp
SUB     save.hlp
SUB     no_tree.hlp


TITLE           ARB: a Short Introduction

OCCURRENCE      General info

DESCRIPTION     ARB (ARBor, Latin: tree): A software environment for maintaining
                databases of molecular sequences and additional information, and
                for analyzing the sequence data, with emphasis on phylogeny
                reconstruction.

                The programs have primarily been developed for ribosomal
                ribonucleic acid (rRNA) sequences and, therefore, contain
                special tools for alignment and analysis of these structures.
                However, other molecular sequence data can also be handled.
                Protein gene sequences and predicted protein primary structures
                as well as protein secondary structures can be stored in the same
                database.

                The ARB package is designed for graphical user
                interface. Program control and data display are available in
                a hierarchical set of windows and subwindows. The majority of
                operations can be controlled using the mouse for moving the
                pointer and the left mouse button for initiating and performing
                operations

SECTION         HOW TO START

                Enter <arb> or <arb filename> to start.

SECTION         ARB MODULES

        ARB_DB

                A central database of (aligned homologous) sequences and
                additional information, taken from public databases or supplied
                by the user, is stored in a (binary or ASCII) file (*.arb).

                All ARB tools for database handling and most ARB tools
                for data analysis act directly upon the database. Any local modifications by
                individual ARB tools are immediately exported to the database
                and all other active tools.

                The database can be structured according to phylogeny or other
                user-defined criteria.

                Tools for text-oriented database searching are integrated.

        ARB_NT  [normally referred to as 'ARB main window']

                Phylogenetic trees derived from the data or imported from other
                sources are displayed within the main window. Different tree
                topologies, complete trees, and subtrees can be stored and used for
                "walking" through the database. Database entries can be
                shown with the tree on the screen or in separate windows.
                Trees can be used to define subsets of data for display
                or analysis by other ARB tools.

                Publication-ready trees can be produced by shaping the
                displayed tree topology and printing or exporting the tree to
                foreign software (TREETOOL [], XFIG []).

                [see LINK{arb_ntree.hlp}]

        ARB_EDIT4

                An editor for the display of sequences and sequence-associated
                data (masks and filters, consensus sequences, higher-order structure) and
                basic editing functions is available. This tool allows manual entering of
                new sequences (with a customized keyboard, if desired); manual modification
                of alignments; search and replacement of sequence stretches; and printout of data.

                Predicted higher-order structure is automatically checked according
                to a user-provided mask and may be displayed with the sequences by
                user-definable symbols.

                [see LINK{e4.hlp}]

        ARB_SECEDIT

                This submodule of ARB_EDIT4 displays the currently selected sequence as
                2D-folded molecule, directly showing the bond in helical regions.

                [see LINK{arb_secedit.hlp}]

        ARB_IMPORT/EXPORT

                ARB modules as well as integrated foreign software (GDE [1],
                READSEQ [2], CONVERTALIGN [3]) can be used for import and export
                of (subsets of) data in different formats, and for database
                merging.

                [see LINK{arb_import.hlp} and LINK{arb_export.hlp}]

        ARB_PROTECTION

                Up to six hierarchical protection levels can be individually
                assigned to database entries to prevent unintended modification
                or loss of data.

                [see LINK{Protection.hlp}]

        ARB_NAMES

                Unique identifiers are automatically generated for the
                individual entries and stored with the database. This prevents
                multiple entries of the same data, and assignment of identical names to different data.

                [see LINK{sp_IDs.hlp}]

        ARB_PHYL

                ARB tools and integrated foreign software (PHYLIP [4], DE SOETE
                [1], fastDNAml [4]) allow calculation of similarity/distance
                matrices, conservation profiles, selection masks and phylogenetic
                tree reconstruction using different treeing approaches.

                [see LINK{phylo.hlp}]

        ARB_PROBE

                Species- and group-specific probes are designed and checked by searching
                the complete database for unique sequence stretches.
                Potential probe or target sites are ranked by user-supplied criteria for mismatch weighing.

                [see LINK{probematch.hlp} and LINK{probedesign.hlp}]

        ARB_PT_SERVER

                The Positional Tree Server provides index-based access to sequence data.
                Supports ARB_PROBE, as well as oligo-based relative search.

                [see LINK{pt_server.hlp}]

        ARB_PARS

                Sequence based reconstruction of phylogenetic trees using the parsimony algorithm.

                [see LINK{arb_pars.hlp}]

        ARB_DIST

                Distance matrix calculation, tree reconstruction based on neighbor joining, and
                topology based clustering.

                [see LINK{dist.hlp} and LINK{di_clusters.hlp}]

        ARB_MERGE

                Allows to load two databases,
                to synchronize the used IDs (ARB_NAMES) and
                to merge data between these databases.

                [see LINK{arb_merge.hlp}]

NOTES           Most ARB tools allow user
                input concerning database structure,
                data selection, inclusion of additional data,
                specification of analysis parameters, and design of simple
                programs for online data analysis. Default values or examples
                are included in the current release.

                Online help is available for all tools (windows).

EXAMPLES        None

WARNINGS        None

BUGS            No bugs known